I received my Ph.D. degree in Computer Science at The Pennsylvania State University, supervised by Professor Mingfu Shao. I received my Master degree in Computer Technology from University of Chinese Academy of Sciences in 2019 and I got my Bachelor degree in Aircraft Airworthiness and Applied Mathematics (minor) from Beihang University in 2016. My CV is here.

Research

My research interests lie in algorithm design and machine learning, and particularly their applications in healthcare and diagnostics. Also, I am interested in designing machine learning models for resource allocation in high throughput computing since I realized that many bioinformatics workflows consists of hundreds or thousands of tasks that vary from short serial tasks to very large parallel tasks.

Currently I am working on designing algorithms and developing softwares for the following research topics:

• transcriptome assembly
• single-cell RNA-seq data analysis

Software

Developed open-source software and tools, such as Scallop2, irtool and Aletsch, have over 15,000 downloads in Bioconda, and the number is actively increasing.

Open source software Scallop2 is an improved reference-based transcriptome assembler that enables accurate assembly of transcriptomes at both single-cell resolution (with Smart-seq3 data) and bulk level (with Illumina paired-end data). Software is available at github and bioconda. Scallop2 has been published at Nature Computational Science.

Open source software Aletsch implements an efficient algorithm to assemble multiple RNA-seq samples (or multiple cells for single-cell RNA-seq data). Software is available at github and bioconda. Alestch has been accepcted by ISMB 2024 and published at Bioinformatics.

Contact

W205, Westgate Building, The Pennsylvania State University, University Park, PA 16802
Email: qqz5133@psu.edu